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Description
Description of feature
Hi, our fastq.gz data provider sequences one sample within multiple lanes and flowcells, and more than one sample can be present in one concrete flowcell+lane combination. For example, for 2 samples (D2077 and M245), pair end files look like this:
D2077_EKDN230048476-1A_H2W7MDSXC_L2_1.fq.gz D2077_EKDN230048476-1A_H2W7MDSXC_L2_2.fq.gz
D2077_EKDN230048476-1A_HFJHGDSX7_L2_1.fq.gz D2077_EKDN230048476-1A_HFJHGDSX7_L2_2.fq.gz
D2077_EKDN230048476-1A_HFTFWDSX7_L4_1.fq.gz D2077_EKDN230048476-1A_HFTFWDSX7_L4_2.fq.gz
D2077_EKDN230048476-1A_HWTLVDSX7_L4_1.fq.gz D2077_EKDN230048476-1A_HWTLVDSX7_L4_2.fq.gz
M245_EKDN230048452-1A_HFJHGDSX7_L2_1.fq.gz MM245_EKDN230048452-1A_HFJHGDSX7_L2_2.fq.gz
MM245_EKDN230048452-1A_HFTFWDSX7_L4_1.fq.gz MM245_EKDN230048452-1A_HFTFWDSX7_L4_2.fq.gz
MM245_EKDN230048452-1A_HWTLVDSX7_L4_1.fq.gz MM245_EKDN230048452-1A_HWTLVDSX7_L4_2.fq.gz
So the same lane number can be present in multiple flowcells (flowcells in my example are H2W7MDSXC,HFJHGDSX7,HFTFWDSX7,HWTLVDSX7). How should I correctly specify the lane column in samplesheet.csv? In sarek, lane can be a string, so in my case, I would for example for the first pair use lane = H2W7MDSXC_L2.